rs10494554

chr1-183146754-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0893 in 152,228 control chromosomes in the GnomAD database, including 1,534 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.089 (1534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13568 AN: 152110 Hom.: 1529 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.00348

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00595

Gnomad OTH AF: 0.0764

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0893 AC: 13592 AN: 152228 Hom.: 1534 Cov.: 32 AF XY: 0.0892 AC XY: 6643 AN XY: 74448

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.0633

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.0469

Gnomad4 FIN AF: 0.00348

Gnomad4 NFE AF: 0.00595

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0513 Hom.: 117

Bravo AF: 0.105

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.4
Dann	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10494554; hg19: chr1-183115889;